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PubMed1988

Distinguishing in vitro electrochemical signatures for norepinephrine and dopamine.

An electrochemical method for the qualitative detection of dopamine and norepinephrine in the presence of serotonin and other purported contaminants in vitro is described. The method uses semidifferential electrochemistry in conjunction with a stearate graphite paste electrode. A method to distinguish electrochemical signatures for specific catecholamines is particularly important because catecholamines are known to have similar oxidation potentials for electrochemical detection. The findings may bear relevance to the interpretation of electrochemical signals from discrete brain nuclei in vivo.

Animals↗

PubMed1996

Identification of an amino acid signature sequence predictive of protein G-inhibitable IgG3-binding activity in group-A streptococcal IgG-binding proteins.

Sequence comparison of six known group-A streptococcal IgG-binding proteins, sharing the common property of protein G-inhibitable IgG3-binding-activity, identified a highly conserved 35-amino-acid (aa) sequence (74-100% similarity) within an EQ-rich central conserved core region of each protein. A search of aa sequence databases identified four additional proteins with > 50% similarity to this consensus sequence. All of these proteins demonstrated protein G-inhibitable IgG3-binding activity. Taken together, these results identify a signature sequence that predicts the presence of a protein G-inhibitable IgG3-binding domain(s) in group-A streptococcal IgG-binding proteins.

Amino Acid Sequence↗

PubMed1994

Harmonic 'signatures' of microorganisms.

The frequency/amplitude effect of various microorganisms exposed to periodic (time varying) electric fields, when proximate to immersed electrodes, has been studied using a novel analytical instrument. The harmonic distribution, in complex signals caused by cells exposed to harmonic free waveforms and occupying part of the electrode/suspension interface volume, was shown to be almost entirely due to the change in the standing interfacial transfer function by the (dielectrically nonlinear) presence of cells. Thus, the characteristic interfacial non-linearity is viewed as variable, being uniquely modulated by the presence of particular cells in the interfacial region. Little can be attributed to bulk (far field) effects. The tendency for subtle (characteristic) signal distortion to occur as a function of particulate (cell or molecular) occupancy of the near electrode interfacial region under controlled current conditions leads to the method of sample characterisation by harmonic (Fourier) analysis. We report here, as a sequel to our original studies (Hutchings et al., 1993; Hutchings and Blake-Coleman, 1993), preliminary results of the harmonic analysis of microbial suspensions under controlled signal conditions using a three-electrode configuration. These data provide three-dimensional graphical representations producing harmonic 'surfaces' for various microorganisms. Thus, cell type differences are characterised by their 'harmonic signature'. The visual distinction provided by these 'surface' forming three-dimensional plots is striking and gives a convincing impression of the ability to identify and enumerate specific microorganisms by acquisition of cell-modulated electrode interfacial Fourier spectra.

Candida↗

PubMed2004

Algorithm-assisted elucidation of disulfide structure: application of the negative signature mass algorithm to mass-mapping the disulfide structure of the 12-cysteine transforming growth factor beta type II receptor extracellular domain.

The power of an algorithm-driven method for interpreting disulfide mass-mapping data is demonstrated in the context of determining the disulfide structure of the extracellular domain of the transforming growth factor beta type II receptor, a 14-kDa cystinyl protein containing 12 cysteines in the form of six disulfide bonds. The disulfide mass-mapping methodology is based on partial reduction and cyanylation-induced cleavage of the cystinyl protein. Because the multiplicity of possible disulfide structures that must be considered grows rapidly with the number of cysteines, as does the difficulty in physically isolating each of the partially reduced and cyanylated isoforms of the analyte, manual data interpretation for disulfide mapping a cystinyl protein containing more than eight cysteines becomes unmanageable. Recently, we introduced the concept of a "negative signature mass algorithm" (NSMA) to determine the disulfide structure of a cystinyl protein by processing an input of its amino acid sequence and mass spectral data from analysis of its associated cyanylation-induced cleavage products. Here, we present experimental results to validate the NSMA concept. A key advantage of the NSMA, in addition to convenience and automation, is its capacity to interpret mass spectra from mixtures of cyanylation-induced cleavage fragments without separating the partially reduced isoforms of the cystinyl protein and without knowledge of the extent of partial reduction.

Algorithms↗

PubMed2006

High variability of Colombian Trypanosoma cruzi lineage I stocks as revealed by low-stringency single primer-PCR minicircle signatures.

In Colombia, high genetic variability has been found among Trypanosoma cruzi stocks isolated from different vector and host species, using isoenzyme analysis and RFLP of total kinetoplastid DNA (kDNA), suggesting that several genetically related T. cruzi populations might be present within a single geographical area or adjacent ones. The objective of this study was to use the low-stringency single primer (LSSP)-PCR technique on variable regions of kDNA minicircles of T. cruzi to determine possible genetic relationships among stocks from distinct geographical regions of Colombia and different vector species and hosts. Although LSSP-PCR analysis showed a high genetic variability among 30 Colombian T. cruzi stocks, 29 of them belonged to T. cruzi lineage I, confirming that this lineage is predominant in different vector and host species from Colombia. Interestingly, one stock isolated from a Pastrongylus geniculatus bug was identified as T. cruzi lineage IIb, using PCR strategies targeted to the intergenic region of miniexon genes, a sequence encoding the D7 domain of the 24salpha ribosomal genes and the A10 fragment, being this finding, the first description of this lineage in Colombia. The LSSP-PCR signatures allowed correlation of most isolates with their respective geographical origins, and in one case from host and vector specimens at a same region, suggesting a transmission event. Moreover, variations in LSSP-PCR profiles among T. cruzi I stocks from a same region suggest that they may have a multiclonal character. Our results show that LSSP-PCR is a fast, valuable technique for characterization of intra-lineage polymorphism among T. cruzi stocks.

Animals↗

PubMed2005

Association between microarray gene expression signature and extravascular matrix patterns in primary uveal melanomas.

PURPOSE: To determine whether there is an association between gene expression profile and looping extravascular matrix patterns in primary uveal melanomas. DESIGN: Laboratory investigation. METHODS: Formalin-fixed, paraffin-embedded sections from 22 primary uveal melanomas that previously were analyzed by microarray gene expression profiling were stained for periodic acid-Schiff and scored in a masked fashion for the presence of looping extravascular matrix patterns. RESULTS: A strong association was observed between looping patterns and the unfavorable class 2 molecular prognostic signature (P < .001). CONCLUSIONS: Looping extravascular matrix patterns occur almost exclusively in class 2 uveal melanomas. This finding may provide new insights into the pathogenesis and management of uveal melanoma.

Gene Expression↗

PubMed2026

Human biopsy-defined ischemia-reperfusion injury-selective reperfusion signature prioritizes reperfusion-timed mitogen-activated protein kinase kinase inhibition after donation after circulatory death liver transplantation.

Early post-liver transplant ischemia-reperfusion injury (IRI) in donation after circulatory death grafts lacks therapies targeted to the immediate postreperfusion window, in part because generic reperfusion transcription obscures IRI-selective amplification. We analyzed paired prereperfusion/postreperfusion liver biopsies from 2 cohorts (GSE151648 and GSE87487) using a difference-in-differences interaction estimand (ΔΔ = [Post-Pre]IRI+ - [Post-Pre]IRI-) to define an IRI-selective early reperfusion program. Genome-wide ΔΔ effects were summarized using pathway-responsive genes, and pathway concordance was tested using permutation (B = 5000). The reproducible ΔΔ footprint highlighted epidermal growth factor receptor-mitogen-activated protein kinase signaling (Spearman ρ = 0.811; P = .001). Directional ΔΔ gene sets (interaction P < .05) were submitted to the L1000 characteristic direction signature search engine2; cross-cohort overlap identified 8 shared perturbagens, including 3 mitogen-activated protein kinase kinase (MEK)1/2 inhibitors. In a hepatic ischemia/reperfusion time course (GSE117915), epidermal growth factor receptor and mitogen-activated protein kinase activities increased within 0.5 hours of reperfusion, and transplant single-cell RNA sequencing (GSE189539) localized MEK/extracellular signal-regulated kinase pathway engagement predominantly to parenchymal cells. A representative MEK inhibitor, PD-0325901, reduced hepatocyte oxygen-glucose deprivation/reoxygenation injury and, when administered at reperfusion in a rat donation after circulatory death liver transplantation model (5-20 mg/kg), attenuated histologic and biochemical injury, apoptosis, and redox-inflammatory readouts and improved 7-day survival. Collectively, this biopsy-anchored ΔΔ interaction-phenotype framework, with cross-cohort concordance as a prespecified robustness gate, nominates reperfusion-timed MEK inhibition as a mechanism- and window-aligned strategy to blunt early post-liver transplant IRI.

difference-in-differences (time × IRI interac↗

PubMed2005

Identification of signatures in biomedical spectra using domain knowledge.

OBJECTIVE: Demonstrate that incorporating domain knowledge into feature selection methods helps identify interpretable features with predictive capability comparable to a state-of-the-art classifier. METHODS: Two feature selection methods, one using a genetic algorithm (GA) the other a L(1)-norm support vector machine (SVM), were investigated on three real-world biomedical magnetic resonance (MR) spectral datasets of increasing difficulty. Consensus sets of the feature sets obtained by the two methods were also assessed. RESULTS AND CONCLUSIONS: Features identified independently by the two methods and by their consensus, determine class-discriminatory groups or individual features, whose predictive power compares favorably with that of a state-of-the-art classifier. Furthermore, the identified feature signatures form stable groupings at definite spectral positions, hence are readily interpretable. This is a useful and important practical result for generating hypothesis for the domain expert.

Algorithms↗

PubMed2006

Unique molecular signatures of glycerophospholipid species in different rat tissues analyzed by tandem mass spectrometry.

Glycerophospholipids (GPL) in animal tissues are composed of a large array of molecular species that mainly differ in the fatty acyl composition. In order to further understand the roles of GPL at the molecular level, it is necessary to have comprehensive, accurate accounts of the molecular makeup for these molecules in animal tissues. However, this task was difficult simply because the conventional technologies of profiling GPL species depended heavily on technical skill for accuracy and reliability and were extremely labor-intensive. In recent years, tandem mass spectrometry (MS/MS) proved to be a highly reliable and sensitive technology for profiling small molecules, including GPL, in biological samples. In this study, we used this technology to perform simultaneous comparative analyses for phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS) and phosphatidylinositol (PI) in the same lipid preparations of liver, lung, kidney, heart, pancreas, stomach, small intestine, spleen, skeleton muscle and brain of an adult rat. We produced molecular profiles of these 4 GPL classes in these 10 different tissues that are highly reproducible between different scans of the same sample and between samples from different animals. It is intriguing that each tissue was found to possess a unique signature of GPL profile that may be used to identify unknown tissues. More importantly, these profiles may also set reference points for studying changes of GPL metabolism in different physiological and pathological conditions.

Animals↗

PubMed2026

Hope is linked with more favorable tumor molecular signatures in serous ovarian cancer.

INTRODUCTION: Hope has been associated with improved quality of life and lower mortality in cancer, but the underlying biological mechanisms are poorly characterized. We previously reported that hope was associated with less inflammation and more normalized diurnal cortisol pre-treatment among women with ovarian cancer. We also reported associations of socio-environmental factors with pro-metastatic processes. Here, we used genome-wide transcriptional profiling to quantify associations between hope and tumor molecular signatures reflecting invasiveness, inflammation, and cellular immunity. METHOD: Participants were 74 women with serous ovarian cancer who provided demographic information and completed surveys pre-surgery. Hope was assessed using a face-valid item from the Center for Epidemiological Studies Depression Scale (CES-D). Depression was assessed using the full CES-D without the hope item. Illumina HT12 microarrays were used to assay tumor RNA, and associations between hope and tumor gene expression were quantified, adjusting for depression, age, BMI, grade, and stage. RESULTS: Adjusting for covariates, hope was associated with multiple favorable differences in RNA expression, including lower levels of mesenchymal differentiation (p = 0.008) and pro-inflammatory gene regulation (NF-κB: p < 0.001; IRF1: p = 0.024; STAT: p = 0.018), elevated epithelial differentiation (p = 0.011), and elevated activity of the IRF7 transcription factor which promotes cellular immunity (p = 0.016). CONCLUSIONS: These data suggest that hope is associated with an ovarian tumor gene expression profile characterized by reduced epithelial-mesenchymal transition (EMT) and inflammatory activity, and increased activity of a transcription factor promoting cellular immunity. These findings highlight potential biological implications of a resilience factor such as hope, but need replication with more robust assessments of hope.

Epithelial mesenchymal transition↗

PubMed2005

GITR overexpression on CD4+CD25+ HTLV-1 transformed cells: detection by massively parallel signature sequencing.

HTLV-I is the etiologic agent of adult T-cell leukemia (ATL), a fatal T-cell malignancy that is associated with profound immunosuppression. In this study, comprehensive gene expression profiling was performed using massively parallel signature sequencing (MPSS) to investigate virus-host interactions in acutely HTLV-1 transformed cells. The analysis revealed the modulation of numerous genes across different functional classes, many of which have not been previously implicated in HTLV-1 transformation or ATL. Differences in the transcriptomes of transformed cell lines were observed that have provided clues on how different clonal populations of cells respond to virus transformation. Quantitation of HTLV-1 transcription was possible, thus making MPSS a useful tool to study emerging pathogens and unknown microbial causes of human diseases. Importantly, overexpression of GITR, an activation marker that has not been previously reported to be upregulated by HTLV-1-infection or in transformed/leukemic cells and that is associated with the suppressor phenotype of CD4+CD25+ regulatory T-cells (Tregs), was also observed. The deep and quantitative gene expression profile generated by MPSS should provide additional leads for discovery research that can be applied to better understand the pathobiology of HTLV-1 transformation and ATL as well as to developing new therapies.

CD4 Antigens↗

PubMed2006

Distinct gene expression signature in Btk-defective T1 B-cells.

Bruton's tyrosine kinase (Btk) is a cytoplasmic tyrosine kinase important for B-lymphocyte maturation. Mutations in Btk give rise to the primary immunodeficiency disease X-linked agammaglobulinemia (XLA) in man and X-linked immunodeficiency (Xid) in mice. Recent studies have subdivided the mouse immature, or transitional, B-cells into two distinct subsets according to their respective surface markers. Transitional type 1 (T1) and transitional type 2 (T2) cells are also located in distinct anatomic locations. Based on a limited number of markers it has previously been reported that the earliest phenotypic sign of Btk deficiency is manifested at the T2 stage in mice. Here, we report on distinct genome-wide transcriptomic signature differences found in T1 B-lymphocytes from Btk-defective compared to normal mice and demonstrate that Btk deficiency is visible already at this stage.

Agammaglobulinaemia Tyrosine Kinase↗

PubMed2026

Myeloma engraftment suppresses osteocytic ossification signatures rescued by loading in mice and reveals predictors of patient outcome.

Multiple myeloma (MM) is a malignant plasma cell disease inducing osteolytic lesions by disrupting bone homeostasis, fostering catabolic and suppressing anabolic functions. While the impact on osteoblast generation and function is well documented, alterations of osteocyte function and extracellular matrix (ECM) are not yet fully understood. Thus, using a syngeneic mouse model of MM by injecting MOPC315.BM cells intratibially into BALB/c mice (n = 95), we performed transcriptomic profiling of an osteocyte-enriched population and identified a mechanosensitive matrisomal gene signature, which was disrupted by tumor engraftment. Non-invasive tibial loading restored the expression of 94 ECM-associated genes, including collagens, fibronectin, and aggrecan. Cross-species integration with RNA-seq data from 387 MM patients revealed eight ECM-related genes whose expression correlated with overall survival (VEGFA, BCAN, FGF13, TNFSF8, SDC1, LAMC1, SEMA3A, and CCL2). Four of these genes (Vegfa, Sdc1, Sema3a, Ccl2) were also load-responsive in a murine osteocyte (IDG-SW3 cells) bioreactor model. Our findings indicate that an existing mechanosensitive osteocytic repair program is suppressed by MM cells, which can be reinvigorated via a brief single loading session. It suggests that exercise-based interventions may be beneficial to restore bone mass through endochondral ossification programs in patients with MM.

Bone disease↗

PubMed2004

Identifying potential prey of the pelagic larvae of the spiny lobster Jasus edwardsii using signature lipids.

Signature lipid analyses were used to identify the natural prey of the pelagic phyllosoma larvae of the spiny lobster Jasus edwardsii. Lipid class, fatty acid and sterol composition were determined for associated potential prey items and for phyllosomes captured between 50 and 90 km offshore from the northeastern coast of New Zealand. Phospholipid was the dominant lipid class in all potential prey items and the transparent phyllosomes. The levels of other lipid classes varied between potential prey items, with the next most abundant classes being triacylglycerols, free fatty acids and sterols. A limited number of the potential prey items also contained wax ester. Major fatty acids in all potential prey items were generally 22:6omega3 (docosahexaenoic acid), 16:0, 18:1omega9c, and 20:5omega3 (eicosapentaenoic acid). Multivariate analyses of fatty acid and sterol content of the samples grouped the phyllosoma samples together regardless of their developmental stage or their collection location. However, the phyllosomes were not associated with any of the general groupings of pelagic ascidians, amphipods, chaetognaths, pteropods, euphausiids, fish, copepods or particulate matter that were formed by the statistical analyses. Although the sterol profiles of the potential prey items showed considerable variation, the phyllosomes contained predominantly cholesterol, suggesting that other dietary sterols are converted to cholesterol or metabolised by the phyllosomes. Therefore, the use of sterols for tracing the prey of J. edwardsii phyllosoma appears to be limited. Our results suggest that phyllosomes are opportunistic predators that feed on a variety of prey and are preferentially retaining specific diet-derived fatty acids.

Animal Feed↗

PubMed2005

Proteinaceous and oligosaccharidic elicitors induce different calcium signatures in the nucleus of tobacco cells.

We previously reported elevated cytosolic calcium levels in tobacco cells in response to elicitors [D. Lecourieux, C. Mazars, N. Pauly, R. Ranjeva, A. Pugin, Analysis and effects of cytosolic free calcium elevations in response to elicitors in Nicotiana plumbaginifolia cells, Plant Cell 14 (2002) 2627-2641]. These data suggested that in response to elicitors, Ca2+, as a second messenger, was involved in both systemic acquired resistance (RSA) and/or hypersensitive response (HR) depending on calcium signature. Here, we used transformed tobacco cells with apoaequorin expressed in the nucleus to monitor changes in free nuclear calcium concentrations ([Ca2+](nuc)) in response to elicitors. Two types of elicitors are compared: proteins leading to necrosis including four elicitins and harpin, and non-necrotic elicitors including flagellin (flg22) and two oligosaccharidic elicitors, namely the oligogalacturonides (OGs) and the beta-1,3-glucan laminarin. Our data indicate that the proteinaceous elicitors induced a pronounced and sustainable [Ca2+](nuc) elevation, relative to the small effects of oligosaccharidic elicitors. This [Ca2+](nuc) elevation, which seems insufficient to induce cell death, is unlikely to result directly from the diffusion of calcium from the cytosol. The [Ca2+](nuc) rise depends on free cytosolic calcium, IP3, and active oxygen species (AOS) but is independent of nitric oxide.

Calcium Signaling↗

PubMed2025

Differentiation latency and dormancy signatures define fetal liver hematopoietic stem cells at single-cell resolution.

Decoding the mechanisms governing the self-renewal of hematopoietic stem cells (HSCs) during their expansion in the fetal liver (FL) could unlock novel therapeutic strategies to expand transplantable HSCs, a long-standing challenge. To explore intrinsic and extrinsic regulation of FL-HSC self-renewal at single-cell resolution, we engineered a culture platform replicating the FL endothelial niche that supports the amplification of serially engraftable HSCs. Leveraging this platform together with single-cell index flow cytometry, live imaging, transplantation assays, and single-cell RNA sequencing, we demonstrate that differentiation latency, cell-division symmetry, and transcriptional signatures of biosynthetic dormancy are distinguishing properties of rare FL-HSCs capable of serial multilineage hematopoietic reconstitution. Our findings support a paradigm in which intrinsic programs and niche-derived signals together facilitate the symmetric self-renewal of FL-HSCs while delaying their active participation in hematopoiesis. Our study also provides a resource for future investigations into intrinsic and extrinsic signaling pathways governing FL-HSC self-renewal.

Hematopoietic Stem Cells↗

PubMed2005

Hydrocarbon and elemental carbon signatures in a tropical wetland: biogeochemical evidence of forest fire and vegetation changes.

Evidence of changing vegetation in the tropical wetland (Rawa Danau, west Java, Indonesia) over the past 7428 years is illustrated by elemental (soot) carbon (EC) and n-alkane composition of sedimentary geolipids. In this study, vegetation changes and relevant controlling factors (e.g. forest fire and climate change) were documented on a decadal to centennial scale. The n-alkane composition that changes with depth might record changes in sources of organic matter (OM) in the wetland. The presence of EC (0.01-0.24% of organic carbon: OC) during late (0-1700 cal. year BP) and mid (3500-4500 cal. year BP) Holocene (at depths 0-50 cm, and 160-210 cm) indicated that large-scale forest fires severely affected the tropical vegetation. The hydrocarbon indices (CPI: carbon preference index, MCN: mean carbon number, and HVI: hydrocarbon vegetation index) significantly correlated with one another while a comparison of EC profile with the profiles of hydrocarbon indices indicated that n-alkane composition of the geolipid in lake sediment could record signatures of changes in catchment vegetation. Forest fire and vegetation changes might be related to regional climatic shifts relating to ENSO activity as well as being influenced by human influences.

Alkanes↗

PubMed2006

Rapid tool for distinction of wines based on the global volatile signature.

This work describes a novel methodology for the rapid distinction of wines by headspace solid-phase microextraction coupled to gas chromatography-mass spectrometry, followed by principal component analysis of the data (HS-SPME-GC-MS-PCA). Headspace SPME is used to extract and concentrate the volatile and semi-volatile fractions. A DB-FFAP fused silica GC capillary column of 30 m at 220 degrees C was used acting as a transfer line of the components sorbed by the Carbowax-divinylbenzene coating fibre to the mass spectrometer, which acts as a sensor (30<m/z<300). In this methodology, which does not require any pre-treatment of the sample, the global volatile signature of the wine headspace (chromatographic profile and m/z pattern of fragmentation in each scan) is evaluated without complete chromatographic separation of its components. In order to retrieve from the data as much chemical information as possible and to extract m/z fragments (markers) for the characterisation and distinction of the wines varieties, a PCA was applied to the data resultant from the unresolved volatile fraction. In the present study, two different monovarietal white wines (Vitis vinifera L. var. Fernão-Pires and Arinto) were tested. Associated to the fast character of the proposed methodology and robustness taking into account the extraction time, it is also important to focus the higher sensibility and the lower effect of the sample moisture of the MS sensor response when compared to the conventional e-noses.

Alcohols↗